Hard to say what was wrong. The sd card itself was ok, the Calibre kobo utilities plugin said the kobo database was ok. If they can somehow come out of sync with each other, then maybe the rebuilding of the database cured the problem, having logged out of the account, or maybe it was re-authorising the device. I didn't try to restore my backup of the database as I didn't need the metadata and I was just happy that all was ok. With KOreader, Plato and NickelMenu, all is better than before now.
